[gmx-users] Re: PME slows down
David van der Spoel
spoel at xray.bmc.uu.se
Thu Jun 2 10:52:27 CEST 2005
> > Hard to say, check energy and density anyway.
> Energy and density are normal.
> > Which gromacs version? Is the machine out of memory?
> v3.2, memory is fine.
> > Are there other jobs running (run top).
> > > >
> > > > > /Jason
> > > > --
> > > > David.
> > > >
> As I mentioned before, the only abnormality I can see are the constraint
> warnings in the log file. Could it be that mdrun is spending more and more
> time in constraint iteration loops?
No, it is not iterative.
Try breaking the jobs in pieces of a few ns. Did you use shuffling or
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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